Stereological Estimation of Dopaminergic Neuron Number in the Mouse Substantia Nigra Using the Optical Fractionator and Standard Microscopy Equipment

The overall goal of this protocol is to describe the design-based stereological estimation of dopaminergic cell number in the mouse SN using standard microscopy equipment. This method is useful to estimate the number of dopaminergic neurons in the mouse substantia nigra for preclinical Parkinson’s disease research using design-based unbiased stereology. The main advantage of this technique is that it can be accomplished with standard microscopy equipment without need for a commercially available complete stereology setup.

Demonstrating the procedure will be Louisa Friez, a technician from my laboratory. Begin by placing a paraformaldehyde fixed mouse brain into a brain matrix and making a cut plus 0.74 millimeters from bregma. Transfer the caudal part of the brain including the SN into 4%PFA in 0.1 molar and fix overnight at four degrees Celsius.

The next day, exchange the PFA for 30%sucrose in 0.1 molar PBS and incubate for another two days at four degrees Celsius to cryo protect the sample. After two days when the brain has sunk in the sucrose, place the tissue into a Cryomold filled with optimal cutting temperature compound and slowly freeze the tissue in liquid dry ice cooled isopentane. Use a cryostat to serially cut 30 micron cryo sections in the coronal plane.

Mark the right hemisphere by puncturing a small hole into the upper region of the brain stem. Collect four series of sections starting at minus 2.46 millimeters from bregma and ending at 4.04 millimeters from bregma. Transfer each series of sections into a tube filled with cryoprotectant and store at minus 20 degrees Celsius.

Capture digital images of tyrosine hydroxylase immunohistochemically stained SN sections using imaging software coupled to a microscope. Start by determining the actual mount and thickness of the sections at three randomly selected counting sites per section. First click on view top offset to define the top of the section.

Then click on stop view top. Thereafter, click on view bottom offset and then click on stop view bottom. Write down the thickness of the section.

Calculate the guard zone by subtracting three microns from the top offset and type the result into the top offset box. Then subtract the 13 micron height of the optical dissector from the top offset number and type the result into the bottom offset box. Select the following parameters, steps 14, size 1.00.

Select the directory to save the file. Click on sequence to start the acquisition. After the images have been acquired, click on processing and select the following parameters, all planes from sequence, montage and the fast and stitching boxes with an image overlap of 10%Start to stitch the images by clicking on start.

This will generate stack images for analysis. To begin, open the image by clicking on file and open. Set the image scale by using the analyze and set scale command.

From this step, change the defined size from pixels to microns. Select the plugins then grid then grid type lines command to randomly insert a grid. Check the random offset box.

Define the size of one square within the grid as 130 microns by 130 microns to equal 16, 900 square microns. Change image type from 16-bit to RGB color by clicking on image then type then RGB color. Locate the substantia nigra pars compacta.

Encircle the region with the paintbrush tool using a brush width of 11. Undo the set scale command by clicking on analyze then set scale then click to remove scale to calculate in pixels rather than microns. Take a screenshot, save the image file and open the new file with ImageJ.

Select brush and a brush width of 25. Mark every grid square that contacts the SN for placement of an optical dissector. Select one grid square that includes parts of the SN.Measure the upper left corner of the square with the cursor in ImageJ to define the starting x and y coordinates.

Select the spreadsheet template entitled optical dissector position and calculate the optical dissector position. Then estimate the cell number using the calculation of cell count spreadsheet as described in the written portion of the protocol. This low power image shows a section of mouse brain after TH staining for dopaminergic neurons.

Higher magnification depicts TH positive dopaminergic neurons. The inset shows the boxed region at increased magnification. This image shows one series of TH stained SN sections covering the whole mouse SN from rostral to caudal.

Each section is separated from the consecutive section by 120 microns. The number of TH positive neurons in the right and left mouse SN were estimated using the method shown in this video and using a commercially available stereology system. As seen here, both methods resulted in comparable cell counts and there were no significant differences between data sets.

Don’t forget that working with paraformaldehyde can be extremely hazardous and precautions such as wearing of personal protection equipment like protective gloves should always be taken while performing this procedure. After watching this video, you should have a good understanding of how to perform unbiased stereological estimation of dopaminergic neuron number in the mouse substantia nigra using the optical fraction method and standard microscopy equipment.